Cilia-associated respiratory (CAR) bacillus is a recently recognized respiratory pathogen of rats and mice. The pathogenesis of CAR bacillus disease has not been investigated thoroughly, and the prevalence of the organism is not known. However, identification of ten colonies with overt CAR bacillus disease by our laboratory in addition to reported cases suggests that infection could be common. Similarities between CAR bacillus disease and murine respiratory mycoplasmosis (MRM), such as parasitism of the surface of ciliated respiratory epithelial cells and the type, distribution, and duration of lesions, suggest that additional similarities probably exist. These include the existence of inapparent infections that may be difficult to detect, and contribution of ancillary factors such as concurrent viral infections to disease expression. If inapparent CAR bacillus infections occur, they could develop into severe respiratory disease under stresses associated with experimentation or concurrent infections acquired in user facilities, adversely affecting the use of rodents in biomedical research. Therefore, our overall objective is to assess the importance of CAR bacillus as a rodent pathogen, especially as a complicating factor in research with rats and mice. Specifically, we will: (i) determine the effects of host genotype, concurrent infection with other respiratory pathogens, exposure to gaseous ammonia, and CAR bacillus strain on expression of CAR bacillus disease in rats and mice; (ii) develop competition and mu-capture ELlSAs of documented sensitivity and specificity that are suitable for large-scale screening of laboratory animals for antibodies to CAR bacillus; and (iii) develop a method, based on amplification of CAR bacillus nucleic acid sequences by the polymerase chain reaction, for detecting CAR bacillus in either fixed, embedded tissues or in fresh tissue samples.